There is no one-click solution to refactor all table names notebooks with UC's three level namespaces. At least, manual updating table names is required during the migration process.
One option is you can you search feature. Search for a table name and filter for Notebooks, then you got list of all notebooks that include the table name, then you can open that notebook in a new tab and update it. Repeat for every table.
Another option is, if you use Databricks Repos and having all your notebooks in your git provider, you can clone to local IDE and use refactor features provided by your IDE. Then update back to your Repos. All your notebooks are just pure files in git, so this is simple and fast to refactor.
There are many other options as well you can choose. However, attention of detail on table names is also required whatever solution you use. Good luck.
